Monday, June 9, 2008

Compendium Review Unit 1 Major Topic: Cells

CELLSI. BASIC CHARACTERISTICS OF LIFEA. 7 CharacteristicsB. Humans are related to other animalsC. Science and social responsibilityII. THE CHEMISTRY OF LIFEA. What are molecules made of?B. Importance of waterC. CarbohydratesD. LipidsE. ProteinsF. Nucleic acidsIII. CELL STRUCTURE AND FUNCTIONA. The fundamental unit of lifeB. Ancestors of animal cellsC. The gateD. The control centerE. The infrastructureF. The powerhouseIV. TISSUE TYPES AND HOMEOSTASISA. Supports and connectsB. Moves and beatsC. Sends, receives and processesD. ProtectsE. The goal of organ systems

THE BASIC CHARACTERISTICS OF LIFEOne of the main points that I have learned from this unit is that life has evolved. The fact that the characteristics of life can be compiled into a short list of seven helps one to understand that all living things were created from the same single cell. It is mind-boggling: Every living thing on this Earth can be identified as living by only seven characteristics. And those 7 characteristics are that living things: 1. Are organized, 2. Take materials and energy from the environment, 3. Reproduce, 4. Grow and develop, 5. Are homeostatic, 6. Respond to stimuli, 7. Have an evolutionary history (Mader 2008). Figure 1.2 from the text (Mader 2008)does a great job in showing how life is organized all the way from an atom up to the Earth's biosphere. The idea of how acquiring materials and energy is needed by all living things can be understood by looking at humans and food intake. Humans eat for many reasons, but the actual need is at the cellular level. Cells need nutrients from food to produce the energy to run the processes that keep them alive. The same is true of a single celled prokaryote. One goal of all living things is to reproduce or to pass on their genes to the next generation. Once a new organism is produced, it must grow and develop so that it can also take in materials, produce energy, and eventually pass on it's genes as well. Along the way, it must maintain homeostasis, so that all of the processes required to produce energy, to grow, to develop, and to reproduce and run normally. If homeostasis is not maintained, proteins will break down, processes will cease, and the internal systems will stop functioning properly. Linked closely to homeostasis is the ability to respond to stimuli. As an organism's outside environment changes, it needs to be able to make adjustments that allow it to maintain homostasis. In order to do this the organism must have a way of notifying its internal systems and then make changes accordingly. And lastly, evolution "explains both the unity and the diversity of life. All organisms share the same characteristics of life because their ancestry can be traced to the first cell or cells. Organisms are diverse because they are adapted to different ways of life" (Mader 2008).

Over time, scientists have developed a classification system into which all organisms can be placed. Taxonomy is built upon the basic fields of morphology, physiology, ecology, and genetics (source1). The system starts with the 3 very broad domains. They are the Eukarya which have a membrane-bounded nucleus and the Archaea and Bacteria which both lack a membrane-bounded nucleus. Within the domain Eukarya are the four kingdoms Animalia, Plantae, Fungi, and Protista. Humans are mammals in the vertebrate class which is part of the kingdom Animalia. Humans are distinguished from other Eukaryotes because we have a nerve cord that is protected by a vertebral column which has repeating units. This indicates that we are segmented animals (Mader 2008).

Part of what separates humans from other mammals also makes us dangerous to our biosphere. We have highly developed brains, we use creative language and we have the ability to use a wide variety of tools. Among others, these factors have allowed us to continue to make significant technological advances over the course of our history. While many of these discoveries have enriched our lives, many have also negatively impacted our environment. Humans are constantly modifying our environment and impacting the biodiversity of our planet.

As mankind continues to make exciting new advances, it becomes increasingly more important for everyone to be educated and take a stand on the ethical issues that these new advances bring to light.

THE CHEMISTRY OF LIFEMolecules, although small in size, can be broken down into even smaller parts. Learning a few basic definitions in chemistry will help to explain this. Matter is anything in this world that has mass and takes up space. It refers to living organisms as well as inanimate objects. One of the basic building blocks of matter then is the element and the smallest unit of an element is the atom. Atoms are made up of protons, neutrons, and electrons. Protons carry a positive charge, electrons carry a negative charge, and neutrons are electrically neutral. The protons and neutrons are located in the nucleus of the atom and the electrons circle the nucleus in electron shells. Atoms are most stable when their outer shell is filled with 8 electrons. Electrons in the outer shell can be shared with other atoms (covalent bonding) or one atom may give up an electron and another atom can accept it (ionic bonding). These two types of bonds are what allow atoms to form molecules and compounds.

One very common compound is water, which is made up of two hydrogen atoms and one oxygen atom. The 6 electrons in the outer shell of the oxygen atom and the 2 electrons (total) from the 2 hydrogen atoms bond covalently to fill the outer shell of each atom. The oxygen atom, because it is a larger atom, has a greater ability to attract the electrons towards it. This causes the water molecule to be polarized, meaning the oxygen side of the molecule has a slightly negative charge and the hydrogen side of the molecule has a slightly positive charge (Mader 2008). Because of this polarity, the hydrogen side of the molecule is attracted to a negatively charged atom, even at some distance away. This attraction is called a hydrogen bond (Mader 2008). Figure 2.7 from the text illustrates the polarity how the polarity of water allows hydrogen bonds to form.The polarity and hydrogen bonding are what allow water to have the following crucial characteristics that are so important to life. 1. Water is liquid at room temperature, so we can drink it. 2. The temperature of liquid water rises and falls slowly, preventing sudden or drastic changes. 3. Water has a high heat of vaporization, keeping the body from overheating. 4. Frozen water is less dense than liquid water so ice floats on water. 5. Water molecules are cohesive, so liquids fill vessels such as blood vessels. 6. Water is a solvent for polar molecules, and thereby facilitates chemical reactions both outside and inside of our bodies (Mader 2008).

Cells in every living organism are composed of four organic molecules or molecules that contain carbon and hydrogen. They are carbohydrates, lipids, proteins, and nucleic acids. When a cell builds or breaks down organic molecules, it uses a dehydration reaction and hydrolysis reaction, respectively. A dehydration reaction removes a hydroxyl group (-OH) and a hydrogen atom (-H) from the subunits that are involved to form the molecule. A water molecule is also formed. A hydrolysis reaction takes a water molecule and adds it back (in the form of a hydroxyl group and a hydrogen atom) to the subunits of the molecule to break it down (Mader 2008).

The first of the four molecules of life is the carbohydrate. Carbohydrate molecules are characterized by the presence of the atomic grouping H-C-OH in which the ratio of hydrogen to oxygen is approximately 2:1. Their purpose is for quick and short-term energy storage in all organisms (Mader 2008). Carbohydrates range in structure from simple to complex. Simple carbohydrates or simple sugars are those that have from 3 to 7 carbon atoms. A disaccaride is also considered a simple sugar. It consists of 2 monosaccarides that have joined together by dehydration. Complex carbohydrates or polysaccharides are macromolecules that contain many glucose units joined together. A few examples of polysaccharides are starch, glycogen, and cellulose (Mader 2008).

The second molecule of life is the lipid, another energy storage molecule, but energy storage is not their most significant function. The most important characteristic of lipids is that they do not dissolve in water because, in general, they are not polarized. Lipids are found as fats and oils, as steroids, and as phospholipids. These three groups of lipids differ from each other in structure and function. When 3 fatty acids (molecule of a carbon-hydrogen chain that ends with the acidic group -COOH) combine with 3 molecules of glycerol by dehydration, a fat molecule and 3 water molecules are produced (Mader 2008). In the body, fat molecules are used for long-term energy storage, insulation, and cushioning. Steroids, on the other hand, are molecules that have a backbone of four fused carbon rings. Steroids differ from each other based on functional groups that are attached to the backbone. One example of a steroid is cholesterol which serves as a component of the plasma membrane in animal cells and is also the precursor to other steroids (Mader 2008). The last group of lipids is the phospholipids. Phospholipids are made up of two fatty acids and a phosphate group. The fatty acids are nonpolar and are therefore hydrophobic. The phosphate group is ionized and is therefore hydrophilic. It is the structure of the phospholipid that allows it to carry out what could arguably be the most significant function that lipids do. The hydrophobic tails and the hydrophylic heads form a bilayer in watery solutions. The tails face towards each other and the heads face the solution. In this way, phospholipds form the plasma membrane of every living cell. The pictorial below taken from this website shows how the phospholipid bilayer can form a plasma membrane.The third molecule of life is the protein. Proteins have many functions, such as providing structural support, catalyzing reactions, transporting substances into and out of the cell, protecting the body by 'attacking' antigens, regulating homeostasis, and causing muscles to contract (Mader 2008). Proteins are made up of subunits called amino acids. An amino acid is made up of a carbon atom that is bonded to a hydrogen atom, an amino group, a acid group and an R group. Amino acids are joined together through peptide bonds. The linear sequence of peptide bonds (polypeptide )is what constitutes the primary structure of the protein. There are at least two and sometimes three additional levels of organization that define a protein. The secondary structure is the orientation that the polypeptide takes on. There are two types: the alpha helix or the pleated sheet. The tertiary structure of a protein is its final three-dimensional shape. Whatever the final shape may be, the hydrophobic sections stay towards the inside while the hydrophilic sections stay towards the outside. When two or more polypeptides join together, the quaternary structure is formed. Not all polypeptides join with others to for the quaternary structure. Figure 2.20 from the text provides an overview of each level.The folding of amino acids into proteins is one area that remains a mystery to scientists. For the most part, they have not been able to figure out why a protein folds up the way it does. Much time, energy and resources have been and still are being put into this field of biology. One example is the Blue Gene project out of IBM and another is the Folding@home, distributed computing project out of Stanford University. This area of study is so important to the understanding, treatment, and possible prevention of many diseases that develop when a protein does not fold up correctly.

Last but not least in the list of molecules of life are the nucleic acids. DNA and RNA are the two types of nucleic acids. The difference in structure between the nucleotides of the two is essentially given in their names. DNA stands for deoxyribonucleic acid and the pentose sugar that it contains is deoxyribose. RNA stands for ribonucleic acid and the sugar that it contains is ribose. The nucleotides of DNA and RNA each also contain a nitrogen-containing base and a phosphate. There are four types of bases in DNA: adenine, thymine, guanine, and cytosine. In RNA uracil replaces thymine (Mader 2008). The other 3 bases are the same. The sugar of one nucleotide bonds with the phosphate of the next to form the backbone of polynucleotide strand (Mader 2008). In DNA, two strands bond via hydrogen bonds between the bases to form a double helix. The same bases always pair together (complementary base pairing): A-T and G-C (Mader 2008). Complementary base pairing allows DNA to replicate in a way that ensures the sequence of bases will remain the same (Mader 2008). It is the sequence of bases that determine the sequence of amino acids in a protein (Mader 2008). RNA is single stranded and forms through complementary base pairing with DNA (Mader 2008). Nucleic acids are also involved in cell metabolism. ATP is adenosine plus three phosphate groups. The first image shown below taken from the text shows the 3 subunits of a nucleotide. The image below it, figure 2.21 from the text, shows the sugar phosphate backbone plus complementary base pairing of DNA.CELL STRUCTURE AND FUNCTIONThe cell theory tells us 3 things: 1. A cell is the basic unit of life, 2. All living things are made up of cells, 3. New cells arise only from preexisting cells. There is much depth behind these three seemingly simple statements. What you can take from these three statements is that the fundamental unit of life, the cell, connects us to all other living things. It is a mind boggling concept. The development of the compound microscope played a huge role in the discoveries that led to the development of the cell theory. In addition to the 2 dimensional, magnified views that the compound microscope provides, scientists today can also view a magnified 3d image of the surface of an object with the use of a scanning electron microscope. Although the image seen with the use of a transmission electron micrscope is only 2d, the magnification power and resolving power are much greater than those of a compound light microscope.

Before diving into a discussion of the many organelles that make up a eukaryotic cell, it is important to understand the origin of these organelles. Unlike eukaryotic cells, the prokaryotes (archaea and bacteria) lack a nucleus. It is believed that the eukaryotic cell evolved from the archaea (Mader 2008). The University of Arizona has an informative and humorous tutorial on Prokaryotes, Eukaryotes, and Viruses. I especially enjoyed this page. It is theorized that the nucleus of the eukaryotic cell was first created from a bit of the plasma membrane breaking off inside the cell and surrounding the DNA. I think of it as a process similar to endocytosis. Figure 3.3 from the text depicts how the evolution from archaea to eukaryote may have occurred. I like to think of the plasma membrane as the gate that surrounds the cell. It provides the boundary between the inside and the outside of the cell. It is the phospholipids that come together to form the bilayer that is the plasma membrane. It keeps the cell intact and is selectively permeable - that is - it only allows certain molecules and ions to enter and exit the cytoplasm freely (Mader 2008). One method by which molecules can cross the membrane freely is by diffusion, which is the movement of molecules from an area of higher concentration to an area of lower concentration. Osmosis is the term used to describe the diffusion of water across the membrane. The 'gate' can not move all the molecules by itself though. This is where the gatekeepers come in. Proteins, or the 'gatekeepers,' embedded in the plasma membrane move molecules from outside the cell to the inside or vice versa using 2 methods, facilitated transport or active transport. The carrier proteins involved in facilitated transport move molecules down their concentration gradient at a rate higher than diffusion. Because the molecules are moving down their concentration gradient, no energy is expended during facilitated diffusion. Active transport on the other hand moves molecules against their concentration gradient. This requires the expenditure of energy. Like facilitated transport, carrier proteins, now called pumps, have an affinity for a certain type of molecule. That is to say that a carrier protein binds with a specific molecule. Two additional methods that move molecules across the membrane are endocytosis and exocytosis. Both involve invagination of the plasma membrane. A pouch is formed around the molecules to be moved and eventually the pouch splits off from the membrane to form a vesicle that houses the molecules. Endocyctosis is the movement of molecules from the outside to the inside of the cell and exocytosis is the movement from the inside to the outside. Figure 3.5 from the text illustrates the fluid-mosaic model of plasma membrane structure.Just as the plasma membrane is the gate that surrounds the cell, in my mind, the nucleus is the control center. The nucleus is where the genetic code is stored in the form of DNA. Remember, it is the genetic code, or the genes, that specify the sequence of the amino acids in proteins (Mader 2008). And proteins control cell metabolism. The nucleus has its own membrane, called the nuclear envelope, separates its contents from that of the rest of the cell. The nuclear envelope is a double membrane that is continuous with the endoplasmic reticulum and contains nuclear pores that allow the passage of ribosomal subunits out of the nucleus and proteins into it (Mader 2008). Through an electron microscope, DNA is only visible in the form of chromatin, which consists of DNA and associated proteins. The nucleus also contains nucleoplasm and nucleoli. The nucleolus is the site of rRNA production and where it joins with proteins to form the subunits of ribosomes (Mader 2008). Figure 3.11 from the text shows a drawing of the nucleus with its various components along with two electron micrographs. The one to the left shows the nuclear pores and the one to the right shows both rough endoplasmic reticulum (ER) and smooth ER. Ribosomes are where protein synthesis occurs. There are ribosomes that are attached directly to the endoplasmic reticulum and others that are floating in the cytoplasm. The endoplasmic reticulum is part of the endomembrane system. The endomembrane system consists of the nuclear envelope, the ER, the Golgi apparatus, lysosomes, and vesicles. Once proteins are synthesized in the ribosomes, they enter the rough ER interior for processing and modification (Mader 2008). The smooth ER produces produces phospholipids and carbohydrates. The Golgi apparatus look like stacks of pancakes and they process, package and delivery proteins and lipids received from the ER. Lysosomes are sacs produced by the Golgi apparatus that contain digestive enzymes. Vesicles are small membranous sacs that transports substances. Figure 3.12 from the text is a great illustration of the endomembrane system. To me, the cytskeleton is the infrastructure of a cell. It provides support, it anchors things down, and it can aid in movement. The cytoskeleton is a collection of protein fibers that crisscross the cytoplasm (Mader 2008). Microtubules, actin filaments and intermediate filaments are all examples of the fibers that make up the cytoskeleton. Cilia and flagella are both made up of microtubules and aid in movement. Cilia are about 20 times shorter than flagella. Ciliated cells line our respiratory tract and a female's oviduct. Sperm cells are flagellated (Mader 2008).

Last but not least is the powerhouse of the cell. So called because mitochondria convert the chemical energy of glucose into energy the cell can use (the chemical energy of ATP molecules) (Mader 2008). This reaction is called cellular respiration. Cellular respiration includes glycolysis, the citric acid cycle and the electron transport chain. During glycolysis (anaerobic), glucose is split into two molecules of pyruvate. NADH results from hydrogen and electrons being removed from glucose. This reaction also nets 2 ATP molecules. The cytric acid cycle (aerobic) completes the breakdown of glucose and again, NADH carries away the hydrogen and electrons and 2 more molecules of ATP are produced. Carrier proteins of the electron transport chain (aerobic) accept the electrons from NADH. The net result of cell respiration is the production of 36 ATP molecules. Proteins, carbohydrates, and lipids can also be used to fuel cellular respiration. Figure 3.14from the text shows a mitochondria. The matrix contains enzymes to break down glucose and ATP production occurs at the cristae.When the body can not bring in enough oxygen to support cellular respiration, it switches to the process of fermentation to produce energy. During fermentation, glycolysis still occurs and the resulting hydrogens and electrons are still passed to NAD. When the electron transport chain is not available due to a lack of oxygen, NADH passes the hydrogens and electrons to pyruvate. The result is the production of lactate and only two molecules of ATP. Fermentation works well for bursts of energy for a short time, but as lactate builds up, muscles begin to fatigue and cramp. The energy that is produced during cell respiration or fermentation is used to power all of the processes that keep it alive. The link to the E.Coli metabolic overview map is a bit overwhelming. I am still trying to get a handle on the fact that all of those processes are happening inside of one bacteria...and that there is a protein that catalyzes each reaction. It is mind boggling.

Tissues are made up of specialized cells of the same type that perform a common function in the body (Mader 208). The first of four tissue types is the connective tissue. The main function of connective tissue is to connect and support. The three types of connective tissue, fibrous, supportive, and fluid, are all made of specialized cells, ground substance, and protein fibers. Fibrous connective tissue can be broken down further into 3 main groups: loose fibrous (protects internal organs), adipose tissue (insulates and protects kidneys and heart), and dense fibrous (tendons, ligaments). Supportive connective tissue includes the cartilages: hyaline (nose, long bones), elastic (ear), and fibrocartilage(disks in back, knee) and bone. Fluid connective tissue consists of blood and lymph. The red blood cells transport oxygen, white blood cells fight infection, and platelets form clots. Lymph is a clear watery fluid derived from tissue fluid that contains white blood cells (Mader 2008).

There are three types of muscle tissue: skeletal, smooth, and cardiac. Skeletal muscle is attached to the skeleton and causes movement in the body when it contracts. Skeletal muscle is striated. Smooth muscle is found in the walls of the viscera (intestine, bladder) and blood vessels (Mader 2008). It contracts slowly and is involuntary. Cardiac muscle is only found in the walls of the heart. Figure 4.5 illustrates and explains the three types of muscle tissue.

Nervous tissue is made up of nerve cells (neurons) and neuroglia, which support and nourish the neurons (Mader 2008). A neuron is made up of three parts. The dendrite receives signals. The cell body houses most of the cytoplasm and the nucleus. The axon conducts nerve impulses. Outside of the brain and spinal cord, fibers (neuron plus myelin) bound by connective tissue form nerves. Neuroglia outnumber neurons nine to one and take up more than half the volume of the brain (Mader 2008).

Epithelial tissue protects. It consists of tightly packed cells that form a tight continuous network. It lines body cavities and covers surfaces. The cells are anchored to a basement membrane. On the other side they are face the environment. Epithelial cells are named based on the number of cell layers and the shape of the cell (Mader 2008). There is also transitional epithelium, which changes in response to tension (urinary bladder), and glandular epithelia secretes a product (goblet cells, sweat glands) (Mader 2008). Figure 4.7 from the text shows some examples of basic epithelial tissue and where you will find each. All of these tissues fit together in different ways to form the organs of the body. As we learned in chapter 1, our organs work together to form the organ systems. It is our organ systems working together that help us to maintain homeostasis. The nervous system processing input from the environment and along with the endocrine system, directs the rest of the organ systems. Figure 4.15 shows a great overview of what each of the major organ systems do to contribute.